GeSICA is a two-step strategy of segmenting the human genome into detailed genomic organizational units. In the first step, GeSICA calculates Interaction Ratio of each genomic bin to dichotomize the human genome into two types of states. Only the functional-related regions are taken into account in the second step — Markov Cluster Algorithm (MCL). And a number of clusters are thus generated. Finally, three types of files are generated as the output of GeSICA: the Interaction-Ratio wiggle file, the segmentation bed file and the MCL genomic clusters file.
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Liu L, Zhang Y, Feng J, Zheng N, Yin J, Zhang Y.
GeSICA: genome segmentation from intra-chromosomal associations.
BMC Genomics 2012; 13:164.